GTModelBeata2015 2020-05-20 13:47
Independent Section Contains tests that are independent of the class of modeled organism, a model's complexity or types of identifiers that are used to describe its components. Parameterization or initialization of the network is not required. See readme for more details.

Consistency


Annotation - Metabolites


Annotation - Reactions


Annotation - Genes


Annotation - SBO Terms





Total Score
87%
Score per Category
0%10%20%30%40%50%60%70%80%90%100%scoreconsistencyannotation_metannotation_rxnannotation_geneannotation_sbosection
Specific Section Covers general statistics and specific aspects of a metabolic network that are not universally applicable. See readme for more details.
SBML
Basic Information
Metabolite Information
Reaction Information
Gene-Protein-Reaction (GPR) Associations
Biomass
Energy Metabolism
Network Topology
Universally Blocked Reactions
154

Universally blocked reactions are reactions that during Flux Variability Analysis cannot carry any flux while all model boundaries are open. Generally blocked reactions are caused by network gaps, which can be attributed to scope or knowledge gaps. Implementation: Use flux variability analysis (FVA) implemented in cobra.flux_analysis.find_blocked_reactions with open_exchanges=True. Please refer to the cobrapy documentation for more information: https://cobrapy.readthedocs.io/en/stable/autoapi/cobra/flux_analysis/ variability/index.html#cobra.flux_analysis.variability. find_blocked_reactions

There are 154 (13.20%) blocked reactions in the model: HYDA, GTHPi, UAG2EMA, UAG2E, UAGCVT, ...


Matrix Conditioning
Experimental Data Comparison
Misc. Tests
Environment